Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007039.1 Hibiscus syriacus cultivar Beakdansim tig00018242_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 57169
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:12074 original size:19 final size:20
Alignment explanation
Indices: 12050--12097 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
12040 ATTTTAAAAA
* *
12050 TAAAAATATT-ATAATATAT
1 TAAAAATATTAAGAAAATAT
12069 TAAAAA-ATTAAGAAAATAT
1 TAAAAATATTAAGAAAATAT
12088 TAAAAATATT
1 TAAAAATATT
12098 GGAAATTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 3 0.12
19 19 0.76
20 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
TAAAAATATTAAGAAAATAT
Found at i:12802 original size:19 final size:19
Alignment explanation
Indices: 12780--12835 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
12770 TATTTTCTTA
12780 TTTAATATACATTGATTTG
1 TTTAATATACATTGATTTG
* *
12799 TTT-ATAT--ATT-TTCTTA
1 TTTAATATACATTGAT-TTG
12815 TTTAATATACATTGATTTG
1 TTTAATATACATTGATTTG
12834 TT
1 TT
12836 GAGATTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
15 1 0.04
16 8 0.29
17 4 0.14
18 4 0.14
19 10 0.36
20 1 0.04
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.59
Consensus pattern (19 bp):
TTTAATATACATTGATTTG
Found at i:12802 original size:35 final size:35
Alignment explanation
Indices: 12763--12835 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
12753 TAAAATTGAA
12763 GTTTATATATTTTCTTATTTAATATACATTGATTT
1 GTTTATATATTTTCTTATTTAATATACATTGATTT
12798 GTTTATATATTTTCTTATTTAATATACATTGATTT
1 GTTTATATATTTTCTTATTTAATATACATTGATTT
12833 GTT
1 GTT
12836 GAGATTTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.60
Consensus pattern (35 bp):
GTTTATATATTTTCTTATTTAATATACATTGATTT
Found at i:12818 original size:16 final size:16
Alignment explanation
Indices: 12764--12822 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
12754 AAAATTGAAG
12764 TTTATATATTTTCTTA
1 TTTATATATTTTCTTA
* *
12780 TTTAATATACATTGAT-TTG
1 TTT-ATAT--ATT-TTCTTA
12799 TTTATATATTTTCTTA
1 TTTATATATTTTCTTA
12815 TTTA-ATAT
1 TTTATATAT
12823 ACATTGATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
15 5 0.15
16 12 0.35
17 4 0.12
18 4 0.12
19 8 0.24
20 1 0.03
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (16 bp):
TTTATATATTTTCTTA
Found at i:12856 original size:16 final size:16
Alignment explanation
Indices: 12831--12874 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
12821 ATACATTGAT
* *
12831 TTGTTGAGATTTAAAA
1 TTGTTAAGATTGAAAA
12847 TTGTTAAGATTGAAAA
1 TTGTTAAGATTGAAAA
12863 TTGTTAAGATTG
1 TTGTTAAGATTG
12875 TATATATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.43
Consensus pattern (16 bp):
TTGTTAAGATTGAAAA
Found at i:14056 original size:60 final size:60
Alignment explanation
Indices: 13958--14124 Score: 151
Period size: 60 Copynumber: 2.7 Consensus size: 60
13948 TACGACCTTT
* * * *** *
13958 ATTTTAAATTAATCTCTAAATTTTTAAATA-TTCTAATTTCAT-CTTTAAATTATAACTA-TC
1 ATTTTAAATTAGTCTC-AAACTTTTAAACATTTC-AATTTCATCCCCCAAAATATAA-TAGTC
*
14018 ATTTTAAATTAGTCCTCAAACTTTTAAACATTTCAATTTTATCCCCCAAAATATAATAGTC
1 ATTTTAAATTAGT-CTCAAACTTTTAAACATTTCAATTTCATCCCCCAAAATATAATAGTC
* * * *
14079 ATTTTAAATTGGTCTCAGAACTTTTTGAACATTCCAATTTTATCCC
1 ATTTTAAATTAGTCTCA-AAC-TTTTAAACATTTCAATTTCATCCC
14125 AAACTACACA
Statistics
Matches: 90, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
60 36 0.40
61 32 0.36
62 22 0.24
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.44
Consensus pattern (60 bp):
ATTTTAAATTAGTCTCAAACTTTTAAACATTTCAATTTCATCCCCCAAAATATAATAGTC
Found at i:14088 original size:61 final size:62
Alignment explanation
Indices: 14008--14124 Score: 168
Period size: 61 Copynumber: 1.9 Consensus size: 62
13998 ATCTTTAAAT
*
14008 TATAACTATCATTTTAAATTAGTCCTCA-AAC-TTTTAAACATTTCAATTTTATCCCCCAAAA
1 TATAACTATCATTTTAAATTAGT-CTCAGAACTTTTTAAACATTCCAATTTTATCCCCCAAAA
* *
14069 TATAA-TAGTCATTTTAAATTGGTCTCAGAACTTTTTGAACATTCCAATTTTATCCC
1 TATAACTA-TCATTTTAAATTAGTCTCAGAACTTTTTAAACATTCCAATTTTATCCC
14125 AAACTACACA
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
60 6 0.12
61 22 0.44
62 22 0.44
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (62 bp):
TATAACTATCATTTTAAATTAGTCTCAGAACTTTTTAAACATTCCAATTTTATCCCCCAAAA
Found at i:15121 original size:2 final size:2
Alignment explanation
Indices: 15116--15175 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
15106 ATATTTTAAT
15116 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15157 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
15176 GAGATTACGT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26234 original size:31 final size:31
Alignment explanation
Indices: 26196--26541 Score: 284
Period size: 31 Copynumber: 11.0 Consensus size: 31
26186 GAACCTCGGC
* * *
26196 AACTGTCCATAGGTCCCAAAAAACCTAGGTA
1 AACTGTCCATATGTCCCGAAAAACATAGGTA
* ** *
26227 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAAAACATAGGTA
* * *
26258 TATTGTCCATATGTCTC-AAAAGACATAGGTA
1 AACTGTCCATATGTCCCGAAAA-ACATAGGTA
* * * *
26289 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTCCCGAAAAACATAGGTA
* * *
26321 TACTATCCATATGTCCCGAAAGACATAGGTA
1 AACTGTCCATATGTCCCGAAAAACATAGGTA
* * * * *
26352 ATTCTGTTCATATGTTCC-ATAGAACATAAGTA
1 A-ACTGTCCATATGTCCCGA-AAAACATAGGTA
* *
26384 TACTGTCCATATGTCCCGAAAGACATAGGTA
1 AACTGTCCATATGTCCCGAAAAACATAGGTA
* * * *
26415 ATTCTGTTCATATGTTCCGTAAAACATAGGTA
1 A-ACTGTCCATATGTCCCGAAAAACATAGGTA
* * *
26447 TACTGTCTATATGTCCCGAAAGACATAGGTA
1 AACTGTCCATATGTCCCGAAAAACATAGGTA
* * * *
26478 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTCCCGAAAAACATAGGTA
*
26510 TACTGTCCATATGTCCC-AAAAGACATAGGTA
1 AACTGTCCATATGTCCCGAAAA-ACATAGGTA
26541 A
1 A
26542 TTCCTCGACT
Statistics
Matches: 239, Mismatches: 67, Indels: 18
0.74 0.21 0.06
Matches are distributed among these distances:
30 4 0.02
31 141 0.59
32 92 0.38
33 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAAAACATAGGTA
Found at i:26312 original size:63 final size:63
Alignment explanation
Indices: 26197--26544 Score: 536
Period size: 63 Copynumber: 5.5 Consensus size: 63
26187 AACCTCGGCA
* * * * *
26197 ACTGTCCATAGGTCCCAAAAAACCTAGGTAA-ACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATATGTCCCAAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
* *
26259 ATTGTCCATATGTCTCAAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
1 ACTGTCCATATGTCCCAAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
* * * * *
26322 ACTATCCATATGTCCCGAAAGACATAGGTAATTCTGTTCATATGTTCCATAGAACATAAGTAT
1 ACTGTCCATATGTCCCAAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
* * *
26385 ACTGTCCATATGTCCCGAAAGACATAGGTAATTCTGTTCATATGTTCCGTAAAACATAGGTAT
1 ACTGTCCATATGTCCCAAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
* *
26448 ACTGTCTATATGTCCCGAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
1 ACTGTCCATATGTCCCAAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
26511 ACTGTCCATATGTCCCAAAAGACATAGGTAATTC
1 ACTGTCCATATGTCCCAAAAGACATAGGTAATTC
26545 CTCGACTCTT
Statistics
Matches: 262, Mismatches: 23, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
62 26 0.10
63 236 0.90
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (63 bp):
ACTGTCCATATGTCCCAAAAGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:29597 original size:17 final size:17
Alignment explanation
Indices: 29575--29616 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
29565 AGGGAATTTA
29575 GAGGCACACATATCAGT
1 GAGGCACACATATCAGT
29592 GAGGCACACATATCAGT
1 GAGGCACACATATCAGT
29609 GAGGCACA
1 GAGGCACA
29617 TATAGATGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.36, C:0.24, G:0.26, T:0.14
Consensus pattern (17 bp):
GAGGCACACATATCAGT
Found at i:33849 original size:16 final size:16
Alignment explanation
Indices: 33828--33858 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
33818 AGAGGCCGAG
33828 ACGTAATTTCGTGGAA
1 ACGTAATTTCGTGGAA
33844 ACGTAATTTCGTGGA
1 ACGTAATTTCGTGGA
33859 GGCTTAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (16 bp):
ACGTAATTTCGTGGAA
Found at i:39853 original size:32 final size:32
Alignment explanation
Indices: 39817--39923 Score: 92
Period size: 32 Copynumber: 3.4 Consensus size: 32
39807 CATTTTCGCT
*
39817 TTCAGATAATGCATAGTAGTGTTAATGTCCCA
1 TTCAGATAATGCATAGTAGTGTTAATGTCACA
** * ** * * * **
39849 TTCAGATAATATACAACAATATCAATGTCGTA
1 TTCAGATAATGCATAGTAGTGTTAATGTCACA
*
39881 TTCA-A-AATGCATAGTAGTGTTAGTGTCACA
1 TTCAGATAATGCATAGTAGTGTTAATGTCACA
39911 TTCAGATAATGCA
1 TTCAGATAATGCA
39924 CATCAGTTAC
Statistics
Matches: 52, Mismatches: 21, Indels: 4
0.68 0.27 0.05
Matches are distributed among these distances:
30 18 0.35
31 2 0.04
32 32 0.62
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (32 bp):
TTCAGATAATGCATAGTAGTGTTAATGTCACA
Found at i:42687 original size:20 final size:20
Alignment explanation
Indices: 42640--43109 Score: 437
Period size: 20 Copynumber: 23.2 Consensus size: 20
42630 AATGACCAAC
42640 AAAATCGCAACGCGATATC--
1 AAAATCGCAACGCGAT-TCAG
* *
42659 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* * **
42679 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
* *
42699 AAGATCGCAACACGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* * *
42721 AGAATCGCAATGCGATTCAT
1 AAAATCGCAACGCGATTCAG
42741 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
42763 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
*
42783 AAAATCGCAACACGATTCAG
1 AAAATCGCAACGCGATTCAG
42803 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
*
42823 AAAATCGCAACGCGGTTCAG
1 AAAATCGCAACGCGATTCAG
42843 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
42865 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
42885 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
42905 AGAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
**
42925 AGGATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
42945 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
**
42965 AGGATCGCAACGCGA-TCAAG
1 AAAATCGCAACGCGATTC-AG
42985 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
43005 AGAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
43025 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
43045 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
**
43065 AGGATCGCAACGCGA-TCAAG
1 AAAATCGCAACGCGATTC-AG
*
43085 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
43105 AAAAT
1 AAAAT
43110 GAGTAAATTC
Statistics
Matches: 380, Mismatches: 43, Indels: 55
0.79 0.09 0.12
Matches are distributed among these distances:
18 3 0.01
19 30 0.08
20 288 0.76
21 10 0.03
22 44 0.12
23 5 0.01
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:43215 original size:6 final size:6
Alignment explanation
Indices: 43204--43255 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
43194 AGACACGTAT
43204 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
43252 GACC
1 GACC
43256 CGAGACGAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:43765 original size:6 final size:6
Alignment explanation
Indices: 43749--43858 Score: 213
Period size: 6 Copynumber: 18.5 Consensus size: 6
43739 TCTCGTCTCG
43749 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
43796 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
43844 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
43859 AATACGTGTC
Statistics
Matches: 104, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.05
6 99 0.95
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:44026 original size:62 final size:61
Alignment explanation
Indices: 43950--44406 Score: 443
Period size: 62 Copynumber: 7.4 Consensus size: 61
43940 GAATTTACTC
* * ***
43950 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGAATTACTGAATCGCAACGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCGATTTTCTGAATCGCGTTGCG
* *
44012 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCGATTTTCTGAATCGCGTTGCG
**
44074 ACGATTCTTGGAAGATCGCGTTGCGATTCTTGG-AATCGCGTTGCGATTTTCTGAATCGCGTTGC
1 A-TTTTC-T-G-A-ATCGCGTTGCGATTCTTGGAAATCGCGTTGCGATTTTCTGAATCGCGTTGC
44138 G
61 G
* *** *
44139 ATTCTT-GGAATCGCGTTGCGATT-TTCTTAATCGCGTTGCGATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCGATTCTTGGAAATCGCGTTGCGATT-TTCTG-A-ATCGCGTTGCG
*
44201 ATTTTCTGAATCGCGTTGCGATT-TTCTG-AATCGCGTTGCGATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTT-GGAAATCGCGTTGCGATTTTCTGAATCGCGTTGCG
* *
44261 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTATGAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAA-ATCGCGTTGCGATTTTCTGAATCGCGTTGCG
* *** * *
44323 ATTCTT-GGAAGATCGCGTTGCGATCTTCTTTTCAA---CGTTGCGCTTTTCTAAATCGCGTTGC
1 ATT-TTCTG-A-ATCGCGTTGCGA--TTCTTGGAAATCGCGTTGCGATTTTCTGAATCGCGTTGC
44384 G
61 G
*
44385 -GTTT-TGATATCGCGTTGCGATT
1 ATTTTCTGA-ATCGCGTTGCGATT
44407 TTGTTGGTCA
Statistics
Matches: 339, Mismatches: 35, Indels: 47
0.81 0.08 0.11
Matches are distributed among these distances:
57 2 0.01
59 15 0.04
60 68 0.20
61 13 0.04
62 161 0.47
63 6 0.02
64 13 0.04
65 34 0.10
66 8 0.02
67 19 0.06
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (61 bp):
ATTTTCTGAATCGCGTTGCGATTCTTGGAAATCGCGTTGCGATTTTCTGAATCGCGTTGCG
Found at i:44032 original size:20 final size:20
Alignment explanation
Indices: 43950--44408 Score: 398
Period size: 20 Copynumber: 22.2 Consensus size: 20
43940 GAATTTACTC
43950 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
43970 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* * ***
43992 AATTACTGAATCGCAACGCG
1 ATTTTCTGAATCGCGTTGCG
*
44012 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
44032 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
*
44054 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
**
44074 ACGATTCTTGGAAGATCGCGTTGCG
1 A-TTTTC-T-G-A-ATCGCGTTGCG
*
44099 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
44119 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
44139 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
44159 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
44179 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
44201 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
44221 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
44241 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
44261 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
44281 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* *
44303 ATTTTATGAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
44323 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* ** *
44345 ATCTTCT-TTTCAACGTTGCG
1 ATTTTCTGAATC-GCGTTGCG
* *
44365 CTTTTCTAAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
44385 -GTTT-TGATATCGCGTTGCG
1 ATTTTCTGA-ATCGCGTTGCG
44404 ATTTT
1 ATTTT
44409 GTTGGTCATT
Statistics
Matches: 358, Mismatches: 48, Indels: 66
0.76 0.10 0.14
Matches are distributed among these distances:
18 2 0.01
19 20 0.06
20 213 0.59
21 36 0.10
22 72 0.20
24 1 0.00
25 14 0.04
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (20 bp):
ATTTTCTGAATCGCGTTGCG
Found at i:44132 original size:40 final size:40
Alignment explanation
Indices: 43950--44408 Score: 377
Period size: 42 Copynumber: 11.1 Consensus size: 40
43940 GAATTTACTC
43950 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
* * ***
43992 AATTACTGAATCGCAACGCGATTTTCTT--AATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGA--TTCTTGGAATCGCGTTGCG
*
44032 ATTCTT-GGAAGATCGCGTTGCGATTTTCTT--AATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCGA--TTCTTGGAATCGCGTTGCG
**
44074 ACGATTCTTGGAAGATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 A-TTTTC-T-G-A-ATCGCGTTGCGATTCTTGGAATCGCGTTGCG
44119 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
*
44159 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
*
44201 ATTTTCTGAATCGCGTTGCGATT-TTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
*
44241 ATTTTCTGAATCGCGTTGCGATT-TTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
* * *
44281 ATTCTT-GGAAGATCGCGTTGCGATT-TTATGAATCGCATTGCG
1 ATT-TTCTG-A-ATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
* **** *
44323 ATTCTT-GGAAGATCGCGTTGCGA-TCTTCTTTTCAACGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCGATTCTTGGAATC-GCGTTGCG
* * *
44365 CTTTTCTAAATCGCGTTGCGGTT-TT-GATATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGA-ATCGCGTTGCG
44404 ATTTT
1 ATTTT
44409 GTTGGTCATT
Statistics
Matches: 358, Mismatches: 37, Indels: 47
0.81 0.08 0.11
Matches are distributed among these distances:
39 11 0.03
40 142 0.40
41 18 0.05
42 144 0.40
43 6 0.02
44 8 0.02
45 29 0.08
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (40 bp):
ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:46062 original size:19 final size:21
Alignment explanation
Indices: 46040--46078 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
46030 TCAAGATGAT
*
46040 AGTTGGAAT-AGTT-ACTACG
1 AGTTGAAATAAGTTGACTACG
46059 AGTTGAAATAAGTTGACTAC
1 AGTTGAAATAAGTTGACTAC
46079 ATTTTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 4 0.24
21 5 0.29
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (21 bp):
AGTTGAAATAAGTTGACTACG
Found at i:50049 original size:38 final size:40
Alignment explanation
Indices: 49991--50065 Score: 127
Period size: 38 Copynumber: 1.9 Consensus size: 40
49981 ATTTATTTTG
*
49991 ATAAAAACAATATTTTAAATATTTGAAT-AAAATAATTTA
1 ATAAAAACAATATTTTAAATATTTAAATAAAAATAATTTA
50030 ATAAAAA-AATATTTTAAATATTTAAATAAAAATAAT
1 ATAAAAACAATATTTTAAATATTTAAATAAAAATAAT
50066 ATATCTATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 19 0.56
39 15 0.44
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (40 bp):
ATAAAAACAATATTTTAAATATTTAAATAAAAATAATTTA
Found at i:51714 original size:16 final size:15
Alignment explanation
Indices: 51689--51723 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
51679 GGGGCAGTTT
51689 GACCCAGTTTTGACCC
1 GACCCAG-TTTGACCC
*
51705 GACCCGGTTTGACCC
1 GACCCAGTTTGACCC
51720 GACC
1 GACC
51724 TGACTGCCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.17, C:0.40, G:0.23, T:0.20
Consensus pattern (15 bp):
GACCCAGTTTGACCC
Done.